https://github.com/edawson/sigprofilerhelper

Helper scripts for the SigProfiler suite of mutational signature analysis tools
https://github.com/edawson/sigprofilerhelper

Last synced: about 2 months ago
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Helper scripts for the SigProfiler suite of mutational signature analysis tools

• Host: GitHub
• URL: https://github.com/edawson/sigprofilerhelper
• Owner: edawson
• Created: 2020-02-26T18:11:26.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2024-02-09T22:46:47.000Z (11 months ago)
• Last Synced: 2024-02-10T04:37:38.704Z (11 months ago)
• Language: Python
• Size: 15.6 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
SigProfilerHelper

-----------------

Eric T. Dawson  

February 2020

## Introduction

SigProfilerHelper provides a set of python command line interface implementations

to the SigProfiler suite of tools (i.e., SigProfilerMatrixGenerator, SigProfilerExtractor, etc).

## Installation

```bash

pip install -r requirements.txt

```

## Basic usage

If you have not already installed a reference, you'll need to install one of the available references from SigProfiler

using the `install_reference.py` script. Here's how to install GRCh38 (GRCh37 is available in the same manner):

### Installing a reference genome:

```bash

python install_reference.py --ref GRCh38

```

### Generating SigProfiler Matrices

To generate the SBS / ID / DNP matrices using SigProfilerMatrixGenerator and place them in a directory called "sigprof\_input":

```bash

python generate_matrix.py -m  -d sigprof_input

```

### Creating seeds for the extraction (optional)

```bash

python create_seeds.py -o seeds.txt -n 1000

```

### Running SigProfilerExtractor

To run SBS96 analysis for 1 to 7 signatures (1000 iterations each) on 16 threads:

```bash

time python scripts/run_sigprofiler.py --gpu --min-iters 1000 --max-iters 10000 -s 1 -e 7 -t sigprof_input/output/SBS/PROJECT.SBS96.all -d 

```

### Full working example with public data:

```bash

## Download and unzip the test data

wget https://public.betulalabs.com/test-data/data_mutations_mod.maf.gz

gunzip data_mutations_mod.maf.gz

## Install your reference

python install_reference.py --ref GRCh37

## Generate the matrix

python generate_matrix.py --maf data_mutations_mod.maf --ref GRCh37 -d data_mutations_output --project Example

## Run sigprofiler

python run_sigprofiler.py -t test_output/output/SBS/PROJECT.SBS96.all -d signatures -s 1 -e 3 --max-iters 10 --min-iters 3 --nmf-replicates 4

```